:GROMOS

Aliphatic and aromatic hydrogen atoms were included implicitly by representing the carbon atom and attached hydrogen atoms as one group centered on the carbon atom, a united atom force field. The van der Waals force parameters were derived from calculations of the crystal structures of hydrocarbons, and on amino acids using short (0.8 nm) nonbonded cutoff radii.W. F. van Gunsteren and H. J. C. Berendsen, Groningen Molecular Simulation (GROMOS) Library Manual, BIOMOS b.v., Groningen, 1987.

In 1996, a substantial rewrite of the software package was released.van Gunsteren, W. F.; Billeter, S. R.; Eising, A. A.; Hünenberger, P. H.; Krüger, P.; Mark, A. E.; Scott, W. R. P.; Tironi, I. G. Biomolecular Simulation: The GROMOS96 Manual and User Guide; vdf Hochschulverlag AG an der ETH Zürich and BIOMOS b.v.: Zürich, Groningen, 1996."The GROMOS Biomolecular Simulation Program Package", W. R. P. Scott, P. H. Huenenberger, I. G. Tironi, A. E. Mark, S. R. Billeter, J. Fennen, A. E. Torda, T. Huber, P. Krueger and W. F. van Gunsteren. J. Phys. Chem. A, 103, 3596–3607. The force field was also improved, e.g., in the following way: aliphatic CH_n groups were represented as united atoms with van der Waals interactions reparametrized on the basis of a series of molecular dynamics simulations of model liquid alkanes using long (1.4 nm) nonbonded cutoff radii."An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase". Journal of Computational Chemistry 22 (11), August 2001, 1205–1218 by Lukas D. Schuler, Xavier Daura, Wilfred F. van Gunsteren. This version is continually being refined and several different parameter sets are available. GROMOS96 includes studies of molecular dynamics, stochastic dynamics, and energy minimization. The energy component was also part of the prior GROMOS, named GROMOS87. GROMOS96 was planned and conceived during a time of 20 months. The package is made of 40 different programs, each with a different essential function. An example of two important programs within the GROMOS96 are PROGMT, in charge of constructing molecular topology and also PROPMT, changing the classical molecular topology into the path-integral molecular topology.

An updated version of the software package was introduced in 2005."The GROMOS software for biomolecular simulation: GROMOS05". Christen M, Hünenberger PH, Bakowies D, Baron R, Bürgi R, Geerke DP, Heinz TN, Kastenholz MA, Kräutler V, Oostenbrink C, Peter C, Trzesniak D, van Gunsteren WF. J Comput Chem 26 (16): 1719–51 {{PMID|16211540}}

The current GROMOS version was released in November 2023 and updated in April 2024. New functionalities such as support fir virtual atoms with non-bonded interactions, shifted reaction-field,{{Cite journal |last=Kubincová |first=Alžbeta |last2=Riniker |first2=Sereina |last3=Hünenberger |first3=Philippe H. |date=2020 |title=Reaction-field electrostatics in molecular dynamics simulations: development of a conservative scheme compatible with an atomic cutoff |url=https://xlink.rsc.org/?DOI=D0CP03835K |journal=Physical Chemistry Chemical Physics |language=en |volume=22 |issue=45 |pages=26419–26437 |doi=10.1039/D0CP03835K |issn=1463-9076|hdl=20.500.11850/454775 |hdl-access=free }} buffer region neural network,{{Cite journal |last=Lier |first=Bettina |last2=Poliak |first2=Peter |last3=Marquetand |first3=Philipp |last4=Westermayr |first4=Julia |last5=Oostenbrink |first5=Chris |date=2022-05-05 |title=BuRNN: Buffer Region Neural Network Approach for Polarizable-Embedding Neural Network/Molecular Mechanics Simulations |url=https://pubs.acs.org/doi/10.1021/acs.jpclett.2c00654 |journal=The Journal of Physical Chemistry Letters |language=en |volume=13 |issue=17 |pages=3812–3818 |doi=10.1021/acs.jpclett.2c00654 |issn=1948-7185 |pmc=9082612 |pmid=35467875}} combined TI with (A-)EDS{{Cite journal |last=Gracia Carmona |first=Oriol |last2=Gillhofer |first2=Michael |last3=Tomasiak |first3=Lisa |last4=De Ruiter |first4=Anita |last5=Oostenbrink |first5=Chris |date=2023-06-13 |title=Accelerated Enveloping Distribution Sampling to Probe the Presence of Water Molecules |url=https://pubs.acs.org/doi/10.1021/acs.jctc.3c00109 |journal=Journal of Chemical Theory and Computation |language=en |volume=19 |issue=11 |pages=3379–3390 |doi=10.1021/acs.jctc.3c00109 |issn=1549-9618 |pmc=10269333 |pmid=37167545}} and selective Gaussian accelerated MD.{{Cite journal |last=Gracia Carmona |first=Oriol |last2=Oostenbrink |first2=Chris |date=2023-09-26 |title=Flexible Gaussian Accelerated Molecular Dynamics to Enhance Biological Sampling |url=https://pubs.acs.org/doi/10.1021/acs.jctc.3c00619 |journal=Journal of Chemical Theory and Computation |language=en |volume=19 |issue=18 |pages=6521–6531 |doi=10.1021/acs.jctc.3c00619 |issn=1549-9618 |pmc=10536968 |pmid=37649349}}

Some of the force field parameter sets that are based on the GROMOS force field. The A-version applies to aqueous or apolar solutions of proteins, nucleotides, and sugars. The B-version applies to isolated molecules (gas phase).

• 54A8{{Cite journal |last=Reif |first=Maria M. |last2=Hünenberger |first2=Philippe H. |last3=Oostenbrink |first3=Chris |date=2012-05-24 |title=New Interaction Parameters for Charged Amino Acid Side Chains in the GROMOS Force Field |url=https://doi.org/10.1021/ct300156h |journal=Journal of Chemical Theory and Computation |volume=8 |issue=10 |pages=3705–3723 |doi=10.1021/ct300156h |issn=1549-9618}} - recalibration of the nonbonded interaction parameters for the charged amino-acid side chains, based on ionic side chain analogs.
• 54A7Schmid N., Eichenberger A., Choutko A., Riniker S., Winger M., Mark A. & van Gunsteren W., "Definition and testing of the GROMOS force-field versions 54A7 and 54B7", European Biophysics Journal, 40(7), (2011), 843–856 [https://dx.doi.org/10.1007/s00249-011-0700-9]. - 53A6 taken and adjusted torsional angle terms to better reproduce helical propensities, altered N–H, C=O repulsion, new CH₃ charge group, parameterisation of Na⁺ and Cl⁻ to improve free energy of hydration and new improper dihedrals.
• 54B7 - 53B6 in vacuo taken and changed in same manner as 53A6 to 54A7.

• 53A5Oostenbrink C., Villa, A., Mark, A. E., and van Gunsteren, W., "A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6", Journal of Computational Chemistry, 25, (2004), 1656–1676 [https://dx.doi.org/10.1002/Jcc.20090]. - optimised by first fitting to reproduce the thermodynamic properties of pure liquids of a range of small polar molecules and the solvation free enthalpies of amino acid analogs in cyclohexane, is an expansion and renumbering of 45A3.
• 53A6 - 53A5 taken and adjusted partial charges to reproduce hydration free enthalpies in water, recommended for simulations of biomolecules in explicit water.

• 45A3Schuler, L. D., Daura, X., and van Gusteren, W. F., An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase, Journal of Computational Chemistry 22(11), (2001), 1205–1218 [https://dx.doi.org/10.1002/jcc.1078]. - suitable to apply to lipid aggregates such as membranes and micelles, for mixed systems of aliphatics with or without water, for polymers, and other apolar systems that may interact with different biomolecules.
• 45A4Soares, T. A., Hünenberger, P. H., Kastenholz, M. A., Kräutler, V., Lenz, T., Lins, R. D., Oostenbrink, C., and van Gunsteren, W. F., An improved nucleic acid parameter set for the GROMOS force field, Journal of Computational Chemistry, 26(7), (2005), 725–737, [https://dx.doi.org/10.1002/jcc.20193]. - 45A3 reparameterised to improve DNA representation.

• 43A1van Gunsteren, W. F., Billeter, S. R., Eking, A. A., Hiinenberger, P. H., Kriiger, P., Mark, A. E., Scott, W. R. P. and Tironi, I. G., Biomolecular Simulation, The GROMOS96 Manual and User Guide, vdf Hochschulverlag AG an der ETH Ziirich and BIOMOS b.v., Zurich, Groningen, 1996.
• 43A2

• [https://www.gromos.net/ GROMOS]
• Ascalaph Designer
• Comparison of software for molecular mechanics modeling
• Comparison of force field implementations

{{Reflist}}

• {{Official website|www.gromos.net}}

{{Chemistry software}}

{{DEFAULTSORT:Gromos}}

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